title: Molecular characterization and complete genome sequence of avian paramyxovirus type 4 prototype strain duck/Hong Kong/D3/75.
abstract: BACKGROUND
  Avian paramyxoviruses (APMVs) are frequently isolated from domestic and wild birds throughout the world. All APMVs, except avian metapneumovirus, are classified in the genus Avulavirus of the family Paramyxoviridae. At present, the APMVs of genus Avulavirus are divided into nine serological types (APMV 1-9). Newcastle disease virus represents APMV-1 and is the most characterized among all APMV types. Very little is known about the molecular characteristics and pathogenicity of APMV 2-9.
  
  
  RESULTS
  As a first step towards understanding the molecular genetics and pathogenicity of APMV-4, we have sequenced the complete genome of APMV-4 strain duck/Hong Kong/D3/75 and determined its pathogenicity in embryonated chicken eggs. The genome of APMV-4 is 15,054 nucleotides (nt) in length, which is consistent with the "rule of six". The genome contains six non-overlapping genes in the order 3'-N-P/V-M-F-HN-L-5'. The genes are flanked on either side by highly conserved transcription start and stop signals and have intergenic sequences varying in length from 9 to 42 nt. The genome contains a 55 nt leader region at 3' end. The 5' trailer region is 17 nt, which is the shortest in the family Paramyxoviridae. Analysis of mRNAs transcribed from the P gene showed that 35% of the transcripts were edited by insertion of one non-templated G residue at an editing site leading to production of V mRNAs. No message was detected that contained insertion of two non-templated G residues, indicating that the W mRNAs are inefficiently produced in APMV-4 infected cells. The cleavage site of the F protein (DIPQR downward arrowF) does not conform to the preferred cleavage site of the ubiquitous intracellular protease furin. However, exogenous proteases were not required for the growth of APMV-4 in cell culture, indicating that the cleavage does not depend on a furin site.
  
  
  CONCLUSIONS
  Phylogenic analysis of the nucleotide sequences of viruses of all five genera of the family Paramyxoviridae showed that APMV-4 is more closely related to the APMVs than to other paramyxoviruses, reinforcing the classification of all APMVs in the genus Avulavirus of the family Paramyxoviridae.
authors.affiliation: Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA. bnayak@umd.edu
authors.forename: Baibaswata
authors.initials: B
authors.lastname: Nayak
authors.forename: Sachin
authors.initials: S
authors.lastname: Kumar
authors.forename: Peter L
authors.initials: PL
authors.lastname: Collins
authors.forename: Siba K
authors.initials: SK
authors.lastname: Samal
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000818:Animals; D018109:Avulavirus / Q000235:genetics* / Q000472:pathogenicity*; D045463:Avulavirus Infections; D002417:Cattle; D002460:Cell Line; D002642:Chick Embryo; D002645:Chickens; D002522:Chlorocebus aethiops; D017124:Conserved Sequence; D006224:Cricetinae; D021901:DNA, Intergenic; D004285:Dogs; D004372:Ducks / Q000821:virology; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D011784:Quail; D012333:RNA, Messenger / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D011817:Rabbits; D017422:Sequence Analysis, DNA; D013552:Swine; D024363:Transcription Initiation Site
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D021901:DNA, Intergenic; D012333:RNA, Messenger; D012367:RNA, Viral